Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations

J Garen (1, 2) , M.J Field (1) , G. Kneller (2, 3) , M. Karplus (4) , J Smith (2)

1 NIH - National Institutes of Health [Bethesda, MD, USA]
2 CEA - Commissariat à l'énergie atomique et aux énergies alternatives
3 IBM - IBM France
4 Harvard University

The internal dynamics of L-alanine in the crystal environment were investigated using molecular dynamics simulations and normal mode calculations. Detailed results are presented for the rotational motion of the methyl and ammonium groups. The rotational barriers and librational frequencies are found to be significantly higher in the crystal than in the isolated molecule. Librational power spectra, calculated from the molecular dynamics simulations by Fourier transformation of the velocity autocorrelation function agree well with the forms and frequencies of the normal modes if the periodic box size used is large enough to avoid unphysical correlations.

Domaines: Physique [physics]

J Garen, M.J Field, G. Kneller, M. Karplus, J Smith. Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations. Journal de Chimie Physique et de Physico-Chimie Biologique, 1991, 88, pp.2587-2596. ⟨10.1051/jcp/1991882587⟩. ⟨hal-02156196⟩